Hello all,
I saw a command in the analysis part of manual in section 8.14
. The command name is g_pvd . It says it can calculate properties like
density of particles per unit volume but I donot find it in the manual
nor in my GROMACS installation. Can anybody help me on this?
Avinash Kumar
Sorry.
I simulate DOPG not POPG.
Thank you anyway.
On Dec 13, 2007 6:53 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> What topology are you using? If you're using one based on the Kartunnen's
> group POPG (the only publicly available one I know of), then be aware that I
> think they saw gel phas
liang wrote:
> Dear Jochen,
>
> Thanks for your information. Can you provide me some references about
> lipid types and properties,
> and the combimation of the recent "popular" membrance proteins (KcsA,
> OmpA, M2, Gramacidin A and Aquaporin) ?
> I have searched several publications, but still did
Ranjani Krishnan wrote:
Hi,
I have noticed that I cannot reproduce MD runs exactly -- running the
exact same .tpr file again gives different results. From previous posts,
I have seen some explanations for this. However, if I do AFM pulling
simulations, I am able to reproduce them exactly –
thanks for your help.
My system ran fine for 250 ps but later the bilayer deformed very much.
my mdp is
integrator = md
dt = 0.002; ps !
nsteps = 125000 ; total 100 ps.
nstcomm = 1
nstxout = 250
nstenergy = 100
n
pragya chohan wrote:
thanks for your help.
My system ran fine for 250 ps but later the bilayer deformed very much.
What was your system preparation protocol - i.e. minimization and
equilibration? See
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
Mark
_
Hello!
I am a new beginner of Gromacs. I am trying to use g_potential to calculate the
potential across the membrane. But I only got the 2D plot (potential vs x
axis). Can I get the 3D plot (potential vs x vs y) by using g_potential?
Thanks in advance for your kind help!
Candy
Hi,
I am running AFM pulling simulations on an integrin-RGD system. I have tried
running the exact same simulation in version 3.3.1 and version 3.3.2, and I
am getting a large VCM message in 3.3.2, but not 3.3.1. Here are the cases
that I have tried:
1) Version 3.2.1: The integrin rec
Hi,
I have noticed that I cannot reproduce MD runs exactly -- running the exact
same .tpr file again gives different results. From previous posts, I have
seen some explanations for this. However, if I do AFM pulling simulations, I
am able to reproduce them exactly - running the same simulation
Hi!
I am attempting to simulate a protein with a modified amino acid using the
Gromacs force field with hydrogens for NMR. I have built the RTP and TOP files
using PRODRG.
I need to know what is the rtp file? relevant to the above force field such
that I can append my rtp file. Is it the ffgmx2
Dear Jayant,
I might be wrong, but I think the original gmx force field that you
are referring to has been deprecated.
Best wishes,
Art
On Dec 14, 2007, at 1:44 PM, jayant_jacques wrote:
Hi!
I am attempting to simulate a protein with a modified amino acid
using the Gromacs force field wi
jayant_jacques wrote:
Hi!
I am attempting to simulate a protein with a modified amino acid using
the Gromacs force field with hydrogens for NMR. I have built the RTP and
TOP files using PRODRG.
I need to know what is the rtp file? relevant to the above force field
such that I can append my rtp
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